Abstract Detail

Phylogenomics

Myint, Sarah [1], Grusz, Amanda [2].

Is one gene enough to determine parental genome dosage in polyploid species?

Despite many new advances in DNA sequencing, one simple approach—genome skimming—continues to be a valuable resource for gathering evolutionary data, especially in recalcitrant taxa with large and/or complex genomes. Here, we push genome skimming to the limit while advancing undergraduate research and training in bioinformatics. Specifically, we leveraged existing genome skimming data to examine patterns of nuclear genome inheritance in the fern Myriopteris yavapensis, a desert-dwelling lineage with a complicated history of whole genome duplication (i.e., polyploidy) and hybridization. We focused on one sample of triploid M. ‘yavapensis’ (2n = 3x) from Pima Co., AZ, to test whether the dosage of parent alleles detected at one nuclear gene (gapCp) is reflected at other nuclear loci in this taxon. To accomplish this aim, we first needed to assess whether our shallow, genome skimming data (Illumina HiSeq 150 bp PE) would provide sufficient coverage to extract low-copy nuclear regions. If so, we aimed to determine patterns of chromosome inheritance in the triploid M. yavapensis. As anticipated, genome skimming provided an impressive amount of chromosomal coverage; for one nuclear locus surveyed, our data were even sufficient to conducft phylogenetic analyses. The resulting phylogeny was consistent with patterns of fixed heterozygosity observed previously at the nuclear gene gapCp. Ultimately, however, coverage was inconsistent among loci and taxa, and we determined that shallow coverage genome skimming is an inappropriate tool for targeting low-copy genomic regions. In the future, we hope that targeted sequencing (e.g., using GoFlag baits) will provide a more reliable avenue to explore genome architecture and evolution in this triploid hybrid fern.

1 - University of Minnesota Duluth, 1035 Kirby Drive, SSB 207, Duluth, Minnesota, 55812, United States
2 - University Of Minnesota Duluth, Biology, 1035 Kirby Drive, SSB 207, Duluth, MN, 55812, United States

Keywords:
Genome skimming
Undergraduate research
Pteridaceae
allopolyploid
Myriopteris yavapensis.

Presentation Type: Poster
Session: P3, Phylogenomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PL023
Abstract ID:1025
Candidate for Awards:None